Preheat the oven to 400 degrees F. Bring a large pot of salted water to boil and cook the ziti until al dente, according to package instructions.
While the pasta is cooking, heat a large skillet over medium-low heat and add the olive oil. Add in the onion, garlic and bell pepper with a big pinch of salt and pepper. Stir in the basil, oregano and red pepper flakes. Cook for 5 minutes, until the veggies are slightly softened. Stir in the zucchini and cook for 3 more minutes. Stir in the tomato paste and red wine.
Pour the marinara sauce into the skillet. Stir in the Parmesan and mix everything together. By now, the pasta should be finished cooking. Drain the pasta and transfer it to a 9x13-inch baking dish. Pour the marinara sauce mixture over the top. Sprinkle on the mozzarella cheese, and toss once or twice to stir it into the pasta.
Break apart the balls of burrata and place the pieces on top of the pasta. Bake for 20 minutes, or until the pasta is golden and bubbly.